Gene detail

Detailed information of g3834.t1 in Montipora capitata

Genomic Location: Sc0000067:173920...193570
NR annotation: CAH3154377.1, unnamed protein product [Porites lobata]
Species Montipora capitata · all data for this species · gene families

Gene Structure

More details in JBrowse

Sequence

CDS

g3834.t1

atggcgaattgcgtcgaattttttgctaaggaaccagctcctgaaaacttgaaagacgtgaaaagtacagtcaccgagtttgcagcatcgcatcgaagaactggaagagatatcgtctttgtgacgtctggaggcacacgtgtaccagtggaggaaaatgccgttcgttttatcgataattttagcattggaacaagaggatctgcctctgctgaatattttctggagcaaggttatgcagtgatatttctacataggcaaggatccctccagccgttcatacgcaactttccctctcatgaagtgctggatcttcttcagctgaaagatttgccagatggatctagccagttagaagttaaccctcgtaaagtgtcaaaagtgacccaggttctcaagatgcatagacaagtacgaatatctggtactctactcatgattgagttcaatagtctttctgagtaccttttcctcctgaggggcgtggctgagtcccttgcgccccatggacccaatgtcatgttgtacctggcagctgctgtctctgacttctacattccatctcaaagcaggcctcaacacaagatttcctctgatgtcccacttcaacttgacttagtgcaggctcctaaaatgatggcacctcttgttaaggaatggattcctcatgctttcatagtttcattcaagttagaaacagatgtgaacattatttccaagaaggcaagaggggccttggccaagtactgtcatcaggtagtggtatccaacatcctccaaacacggaaaaagactgttgtgataattacaccaacccaagagacggccatatggatgtcagactcagaactagaggctggcagagaaatagaggaaaagattgttgctgaccttaagaaaatgcatcagcagtttatagcttcctcggggatgcaaggtaatggcaagtcagtcattgcgtcagatcaggtaccatctaatttccaggttggacagtttatcaccactcagatacaagccctttcttctcagaattctgatagcattatttcaggctttgcctcttacaccattccaacagcttctcttggcctccctcccacttcagcagtgtctcaaatccaagcgtcaaaaaatgaggaagtgtccacagctcaagaaatcacccaaggcaatgagccagacatgtctgacctgtctggttcctccggccagttgtttggtactttgtcagatacttgcttgacgccagatatgaaagactttatagagtcattcagagcacgacgaatcgcactgggatacactcaggaagatgttggtaatgagctttcccacaccaatggacattcttcttacagtcaatccttcatctctcgatttgaatccaaaaatcttggtttaaaggctgcagagaaaatgaagccagtgttgcaggcatggatagaacaaaaggagcaagagtgtgcaaaggggttacgcatgtgcaaaaagcgcaaaagaagaacttccttttcaaatgaaactctgcagtgtttgattcacagttttgaacagaatccaaagcctaccagtgctgaaatagtggaaatatcttccaagttaggcctggagccagttactgtgagagtttggttctgcaatcgaaaacaaatgatgaagcgaatggctactggaaaagtacgtgctgttcattctctcaaagcagaacttgatgcaaagaaacaagatgagcaaatcccagaggaaaaagagccccaagctaagttggacttcaccaacatgccagtggggcagttctccttcacagaggatcgtgtaaaagcccttgtatgtttgacctctgatggaagccccatgaaaagctctcatccagcaacatcctctacagctgtcagctatgctcaggctcatgatgacagcatcatccatgctgacccaggagctcggaacactatgcaggagaaacctcagctgattgagaagggatctcctgctgcaatccagtatgggcaaagcaaggtacaatttcccttggtccgaaatgggcctaatggtgtcacttcttttgattcagtctcaaatgtggctatgactggttcataa

Transcript

g3834.t1

ATGGCGAATTGCGTCGAATTTTTTGCTAAGGAACCAGCTCCTGAAAACTTGAAAGACGTGAAAAGTACAGTCACCGAGTTTGCAGCATCGCATCGAAGAACTGGAAGAGATATCGTCTTTGTGACGTCTGGAGGCACACGTGTACCAGTGGAGGAAAATGCCGTTCGTTTTATCGATAATTTTAGCATTGGAACAAGAGGATCTGCCTCTGCTGAATATTTTCTGGAGCAAGGTTATGCAGTGATATTTCTACATAGGCAAGGATCCCTCCAGCCGTTCATACGCAACTTTCCCTCTCATGAAGTGCTGGATCTTCTTCAGCTGAAAGATTTGCCAGATGGATCTAGCCAGTTAGAAGTTAACCCTCGTAAAGTGTCAAAAGTGACCCAGGTTCTCAAGATGCATAGACAAGTACGAATATCTGGTACTCTACTCATGATTGAGTTCAATAGTCTTTCTGAGTACCTTTTCCTCCTGAGGGGCGTGGCTGAGTCCCTTGCGCCCCATGGACCCAATGTCATGTTGTACCTGGCAGCTGCTGTCTCTGACTTCTACATTCCATCTCAAAGCAGGCCTCAACACAAGATTTCCTCTGATGTCCCACTTCAACTTGACTTAGTGCAGGCTCCTAAAATGATGGCACCTCTTGTTAAGGAATGGATTCCTCATGCTTTCATAGTTTCATTCAAGTTAGAAACAGATGTGAACATTATTTCCAAGAAGGCAAGAGGGGCCTTGGCCAAGTACTGTCATCAGGTAGTGGTATCCAACATCCTCCAAACACGGAAAAAGACTGTTGTGATAATTACACCAACCCAAGAGACGGCCATATGGATGTCAGACTCAGAACTAGAGGCTGGCAGAGAAATAGAGGAAAAGATTGTTGCTGACCTTAAGAAAATGCATCAGCAGTTTATAGCTTCCTCGGGGATGCAAGGTAATGGCAAGTCAGTCATTGCGTCAGATCAGGTACCATCTAATTTCCAGGTTGGACAGTTTATCACCACTCAGATACAAGCCCTTTCTTCTCAGAATTCTGATAGCATTATTTCAGGCTTTGCCTCTTACACCATTCCAACAGCTTCTCTTGGCCTCCCTCCCACTTCAGCAGTGTCTCAAATCCAAGCGTCAAAAAATGAGGAAGTGTCCACAGCTCAAGAAATCACCCAAGGCAATGAGCCAGACATGTCTGACCTGTCTGGTTCCTCCGGCCAGTTGTTTGGTACTTTGTCAGATACTTGCTTGACGCCAGATATGAAAGACTTTATAGAGTCATTCAGAGCACGACGAATCGCACTGGGATACACTCAGGAAGATGTTGGTAATGAGCTTTCCCACACCAATGGACATTCTTCTTACAGTCAATCCTTCATCTCTCGATTTGAATCCAAAAATCTTGGTTTAAAGGCTGCAGAGAAAATGAAGCCAGTGTTGCAGGCATGGATAGAACAAAAGGAGCAAGAGTGTGCAAAGGGGTTACGCATGTGCAAAAAGCGCAAAAGAAGAACTTCCTTTTCAAATGAAACTCTGCAGTGTTTGATTCACAGTTTTGAACAGAATCCAAAGCCTACCAGTGCTGAAATAGTGGAAATATCTTCCAAGTTAGGCCTGGAGCCAGTTACTGTGAGAGTTTGGTTCTGCAATCGAAAACAAATGATGAAGCGAATGGCTACTGGAAAAGTACGTGCTGTTCATTCTCTCAAAGCAGAACTTGATGCAAAGAAACAAGATGAGCAAATCCCAGAGGAAAAAGAGCCCCAAGCTAAGTTGGACTTCACCAACATGCCAGTGGGGCAGTTCTCCTTCACAGAGGATCGTGTAAAAGCCCTTGTATGTTTGACCTCTGATGGAAGCCCCATGAAAAGCTCTCATCCAGCAACATCCTCTACAGCTGTCAGCTATGCTCAGGCTCATGATGACAGCATCATCCATGCTGACCCAGGAGCTCGGAACACTATGCAGGAGAAACCTCAGCTGATTGAGAAGGGATCTCCTGCTGCAATCCAGTATGGGCAAAGCAAGGTACAATTTCCCTTGGTCCGAAATGGGCCTAATGGTGTCACTTCTTTTGATTCAGTCTCAAATGTGGCTATGACTGGTTCATAA

Protein

UniProt (Swiss-Prot top hit)

UniProt accession	Description
Q8VDG5	Phosphopantothenate--cysteine ligase OS=Mus musculus OX=10090 GN=Ppcs PE=1 SV=1
Q9HAB8	Phosphopantothenate--cysteine ligase OS=Homo sapiens OX=9606 GN=PPCS PE=1 SV=2
Q9LZM3	Phosphopantothenate--cysteine ligase 2 OS=Arabidopsis thaliana OX=3702 GN=PPCS2 PE=2 SV=2

Gene family

Family type	Membership / link
Orthogroup (gene family)	OG0006300 (this species only) · gene tree & orthology

Pfam domain

Pfam accession	Pfam name	Description	Type	Source
PF04127 all species →	DFP	DNA / pantothenate metabolism flavoprotein	Family	Interproscan
PF00046 all species →	Homeodomain	Homeodomain	Domain	Interproscan
PF00157 all species →	Pou	Pou domain - N-terminal to homeobox domain	Domain	Interproscan

InterPro

InterPro term	Type	Description	Source
IPR009057 all species →	Homologous_superfamily	Homeobox-like domain superfamily	Interproscan
IPR050255 all species →	Family	POU domain transcription factor	Interproscan
IPR013847 all species →	Domain	POU domain	Interproscan
IPR001356 all species →	Domain	Homeobox domain	Interproscan
IPR007085 all species →	Domain	DNA/pantothenate metabolism flavoprotein, C-terminal	Interproscan
IPR010982 all species →	Homologous_superfamily	Lambda repressor-like, DNA-binding domain superfamily	Interproscan
IPR000327 all species →	Domain	POU-specific domain	Interproscan
IPR035929 all species →	Homologous_superfamily	CoaB-like superfamily	Interproscan
IPR017970 all species →	Conserved_site	Homeobox, conserved site	Interproscan

PANTHER

PANTHER term	Description	Source
PTHR11636 all species →	POU DOMAIN	Interproscan

Gene Ontology

GO term	Category	Description	Source
GO:0000978 all species →	Molecular Function	RNA polymerase II cis-regulatory region sequence-specific DNA binding	Interproscan
GO:0000981 all species →	Molecular Function	DNA-binding transcription factor activity, RNA polymerase II-specific	Interproscan
GO:0006357 all species →	Biological Process	regulation of transcription by RNA polymerase II	Interproscan
GO:0003677 all species →	Molecular Function	DNA binding	Interproscan
GO:0003700 all species →	Molecular Function	DNA-binding transcription factor activity	Interproscan
GO:0006355 all species →	Biological Process	regulation of DNA-templated transcription	Interproscan

Search by domain instead of by gene. Any accession above (InterPro, Pfam, PANTHER, GO, KEGG) can be used as a query on the Functional Domain Search page, which searches all 148 annotated genomes at once.

KEGG pathway

KO	Enzyme	Enzyme ID	Pathway	Map ID	Source
K01922	PPCS, COAB; phosphopantothenate---cysteine ligase (ATP)	EC:6.3.2.51	Pantothenate and CoA biosynthesis	ko00770	deepkoala

Searching by KO or pathway ID across all species is available on the KEGG Pathway page.

Expression pattern (RNA-seq)

Transcript abundance of g3834.t1 across 48 RNA-seq samples of Montipora capitata. Values are TPM (transcripts per million) from the StringTie quantification; one bar is one sample, grouped and coloured by condition, sorted by expression within each group.

48Samples

48TPM > 0

3Conditions

42.2Max TPM

14.3Mean TPM

By condition

Condition	Samples	TPM > 0	Mean TPM	Max TPM
whole organisms · ambient pH treatment	21	21	14.12	42.24
whole organisms · low pH treatment	15	15	13.95	31.23
whole organisms · extra low pH treatment pH treatment	12	12	15.13	36.52

Per sample · hover a bar for the full sample record · show / hide the sample table

SRA run	Condition	Tissue	Developmental stage	Treatment	Study	TPM
SRR11452230	whole organisms · ambient pH treatment	whole organisms	planulae	ambient pH treatment	SRP254626	42.24
SRR11452222	whole organisms · ambient pH treatment	whole organisms	planulae	ambient pH treatment	SRP254626	32.74
SRR11452228	whole organisms · ambient pH treatment	whole organisms	planulae	ambient pH treatment	SRP254626	30.93
SRR11452252	whole organisms · ambient pH treatment	whole organisms	prawn chip	ambient pH treatment	SRP254626	26.79
SRR11452246	whole organisms · ambient pH treatment	whole organisms	prawn chip	ambient pH treatment	SRP254626	26.64
SRR11452232	whole organisms · ambient pH treatment	whole organisms	blastula	ambient pH treatment	SRP254626	23.68
SRR11452250	whole organisms · ambient pH treatment	whole organisms	prawn chip	ambient pH treatment	SRP254626	22.49
SRR11452231	whole organisms · ambient pH treatment	whole organisms	blastula	ambient pH treatment	SRP254626	17.37
SRR11452237	whole organisms · ambient pH treatment	whole organisms	gastrula	ambient pH treatment	SRP254626	11.35
SRR11452259	whole organisms · ambient pH treatment	whole organisms	cleavage	ambient pH treatment	SRP254626	10.88
SRR11452260	whole organisms · ambient pH treatment	whole organisms	cleavage	ambient pH treatment	SRP254626	10.28
SRR11452243	whole organisms · ambient pH treatment	whole organisms	gastrula	ambient pH treatment	SRP254626	8.34
SRR11452254	whole organisms · ambient pH treatment	whole organisms	cleavage	ambient pH treatment	SRP254626	7.65
SRR11452242	whole organisms · ambient pH treatment	whole organisms	gastrula	ambient pH treatment	SRP254626	5.30
SRR11452263	whole organisms · ambient pH treatment	whole organisms	egg	ambient pH treatment	SRP254626	5.09
SRR11452251	whole organisms · ambient pH treatment	whole organisms	egg	ambient pH treatment	SRP254626	4.88
SRR11452217	whole organisms · ambient pH treatment	whole organisms	fertilized embryo	ambient pH treatment	SRP254626	3.66
SRR11452262	whole organisms · ambient pH treatment	whole organisms	egg	ambient pH treatment	SRP254626	2.83
SRR11452233	whole organisms · ambient pH treatment	whole organisms	morula	ambient pH treatment	SRP254626	1.21
SRR11452240	whole organisms · ambient pH treatment	whole organisms	fertilized embryo	ambient pH treatment	SRP254626	1.11
SRR11452234	whole organisms · ambient pH treatment	whole organisms	morula	ambient pH treatment	SRP254626	1.07
SRR11452223	whole organisms · low pH treatment	whole organisms	planulae	low pH treatment	SRP254626	31.23
SRR11452224	whole organisms · low pH treatment	whole organisms	planulae	low pH treatment	SRP254626	25.23
SRR11452221	whole organisms · low pH treatment	whole organisms	planulae	low pH treatment	SRP254626	24.30
SRR11452247	whole organisms · low pH treatment	whole organisms	prawn chip	low pH treatment	SRP254626	22.63
SRR11452245	whole organisms · low pH treatment	whole organisms	prawn chip	low pH treatment	SRP254626	22.11
SRR11452249	whole organisms · low pH treatment	whole organisms	prawn chip	low pH treatment	SRP254626	21.49
SRR11452236	whole organisms · low pH treatment	whole organisms	gastrula	low pH treatment	SRP254626	8.53
SRR11452238	whole organisms · low pH treatment	whole organisms	gastrula	low pH treatment	SRP254626	8.41
SRR11452241	whole organisms · low pH treatment	whole organisms	gastrula	low pH treatment	SRP254626	7.89
SRR11452253	whole organisms · low pH treatment	whole organisms	cleavage	low pH treatment	SRP254626	7.06
SRR11452218	whole organisms · low pH treatment	whole organisms	fertilized embryo	low pH treatment	SRP254626	7.02
SRR11452255	whole organisms · low pH treatment	whole organisms	cleavage	low pH treatment	SRP254626	6.68
SRR11452258	whole organisms · low pH treatment	whole organisms	cleavage	low pH treatment	SRP254626	6.55
SRR11452216	whole organisms · low pH treatment	whole organisms	fertilized embryo	low pH treatment	SRP254626	5.28
SRR11452229	whole organisms · low pH treatment	whole organisms	fertilized embryo	low pH treatment	SRP254626	4.93
SRR11452225	whole organisms · extra low pH treatment pH treatment	whole organisms	planulae	extra low pH treatment pH treatment	SRP254626	36.52
SRR11452227	whole organisms · extra low pH treatment pH treatment	whole organisms	planulae	extra low pH treatment pH treatment	SRP254626	36.07
SRR11452226	whole organisms · extra low pH treatment pH treatment	whole organisms	planulae	extra low pH treatment pH treatment	SRP254626	25.20
SRR11452248	whole organisms · extra low pH treatment pH treatment	whole organisms	prawn chip	extra low pH treatment pH treatment	SRP254626	22.72
SRR11452244	whole organisms · extra low pH treatment pH treatment	whole organisms	prawn chip	extra low pH treatment pH treatment	SRP254626	20.79
SRR11452256	whole organisms · extra low pH treatment pH treatment	whole organisms	cleavage	extra low pH treatment pH treatment	SRP254626	9.32
SRR11452235	whole organisms · extra low pH treatment pH treatment	whole organisms	gastrula	extra low pH treatment pH treatment	SRP254626	7.82
SRR11452239	whole organisms · extra low pH treatment pH treatment	whole organisms	gastrula	extra low pH treatment pH treatment	SRP254626	7.14
SRR11452220	whole organisms · extra low pH treatment pH treatment	whole organisms	fertilized embryo	extra low pH treatment pH treatment	SRP254626	5.64
SRR11452257	whole organisms · extra low pH treatment pH treatment	whole organisms	cleavage	extra low pH treatment pH treatment	SRP254626	3.95
SRR11452219	whole organisms · extra low pH treatment pH treatment	whole organisms	fertilized embryo	extra low pH treatment pH treatment	SRP254626	3.54
SRR11452261	whole organisms · extra low pH treatment pH treatment	whole organisms	fertilized embryo	extra low pH treatment pH treatment	SRP254626	2.81

Source: CnidoSite RNA-seq expression matrices (MCAPI_TPM, StringTie quantification over 48 runs), joined to SRA sample metadata. Samples whose tissue/treatment is not recorded in the source metadata are grouped by the descriptor carried in the expression matrix itself.